Contacts of the strand formed by residues 913 - 917 (chain A) in PDB entry 4AGD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET 913 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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831A ARG* 4.6 12.3 - - - +
834A LEU* 4.6 16.4 - - - -
836A LEU* 4.8 11.7 - - + -
867A VAL* 3.9 25.4 - - + -
868A LYS 3.5 4.0 - - - -
869A MET* 3.7 20.6 - - + +
904A ALA* 3.2 5.7 - - - +
905A CYS* 2.9 47.6 + - + +
911A PRO* 3.4 41.1 - - + +
912A LEU* 1.3 88.1 - - - +
914A VAL* 1.3 63.6 + - - +
915A ILE* 3.9 3.2 + - + +
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Residues in contact with VAL 914 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866A ALA 3.8 0.7 - - - +
867A VAL* 3.4 1.6 - - - -
868A LYS* 2.7 51.1 + - + +
882A LEU* 3.7 25.4 - - + +
885A GLU* 5.6 0.7 - - + -
886A LEU* 3.7 33.7 - - + +
889A LEU* 3.7 22.0 - - + -
901A LEU* 3.3 27.1 - - + -
903A GLY 4.0 2.0 - - - -
904A ALA* 4.6 1.1 - - - +
912A LEU* 4.9 3.6 - - + -
913A MET* 1.3 74.8 - - - +
915A ILE* 1.3 58.8 + - - +
916A VAL* 3.9 6.0 - - + +
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Residues in contact with ILE 915 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829A PHE* 4.2 18.4 - - + -
834A LEU* 4.6 10.5 - - + -
856A ILE* 3.8 17.9 - - + -
865A VAL* 3.6 34.8 - - + -
866A ALA 3.6 3.4 - - - +
867A VAL* 4.3 15.0 - - + -
901A LEU* 3.1 8.5 - - - +
902A LEU* 2.5 32.3 + - + -
903A GLY 2.7 32.5 + - - +
904A ALA* 4.1 2.7 - - - +
905A CYS* 4.0 27.4 - - - -
913A MET* 4.2 2.5 - - + +
914A VAL* 1.3 75.4 - - - +
916A VAL* 1.3 58.6 + - - +
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Residues in contact with VAL 916 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866A ALA* 2.8 44.5 + - + +
868A LYS* 4.3 16.4 - - + -
889A LEU* 4.0 15.9 - - + -
899A VAL* 3.6 11.4 - - + -
900A ASN 3.2 13.5 - - - +
901A LEU* 4.2 2.7 - - - -
902A LEU* 3.7 12.5 - - - +
914A VAL* 3.9 20.4 - - + -
915A ILE* 1.3 80.5 - - - +
917A GLU* 1.3 66.0 + - - +
918A PHE 3.3 0.3 + - - -
2000A B49 3.5 30.3 - - + -
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Residues in contact with GLU 917 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866A ALA 4.4 0.2 - - - -
894A HIS* 5.3 3.6 - - - -
899A VAL* 4.1 2.7 - - + +
900A ASN* 2.8 48.9 + - - +
902A LEU* 4.1 19.0 - - + +
916A VAL* 1.3 74.1 - - - +
918A PHE* 1.3 63.3 + - - +
919A CYS* 4.0 3.3 - - - -
1043A LYS* 2.8 46.3 + - + +
2000A B49 2.9 25.5 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il